Structure and life cycle of viruses

Definition

A virus is a parasitic pathogenic microorganism consisting of a protein coat called a capsid that surrounds genetic material, which can be either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Each virus type carries out a life cycle tailored to that particular organism, but in general, the process begins with the entrance of the virus’s genetic material into the host cell, the replication of the viral genome, and the viral genome’s packaging within newly produced capsid proteins.

Structural Characteristics

The individual virus particle, known as a virion, consists of genetic material, either DNA or RNA, surrounded by a protein coat called a capsid. Some viruses also include an external lipid envelope generally obtained by budding through a cell membrane during the assembly process. Both the morphology (physical shape) or appearance of the virus and the presence of a viral envelope are genetically determined. The morphology of virus particles encompasses many sizes, ranging from 20 nanometers (nm) in diameter for the smallest viruses, such as those that are the etiological agents for the common cold (rhinoviruses) or certain forms of hepatitis (hepatitis A virus), to the largest and most complex viruses in the 500 nm range (smallpox virus). The poxviruses are large enough to be observed with conventional light microscopes. By comparison, the average-size bacterium is approximately 1 to 2 micrometers (m) in diameter, or roughly two to four times larger than the largest viruses, and a blood cell is approximately 20 m in diameter.

Viruses are limited in the quantity of genetic material they carry. Consequently, the most efficient means to encode the proteins that will be used for the capsid is to utilize repeating protein units known as protomers, which can self-assemble into the subunits, or capsomeres, of the capsid. The result of utilizing repeating units is that the morphological symmetry will be one of two forms: icosahedral (cuboidal) or helical. The only exception is found among the large poxviruses that exhibit a more complex symmetry, reflecting their ability to encode more than two hundred proteins.

Helical capsids resemble long hollow tubes in which the genome is in the center and capsomeres are arranged in a helical fashion around the core. All known helical viruses contain RNA as the genetic material. Examples of helical viruses include some bacterial viruses, the tobacco mosaic virus (TMV), influenza virus, and measles virus. The helical capsid for some viruses, including measles and influenza, is enclosed within a viral envelope.

Icosahedral-shaped viruses have twenty faces, each an equilateral triangle, and twelve corners or vertices. These viruses exhibit what is known as 5:3:2 symmetry, representing the symmetry exhibited by respective axes of the virus. Capsomeres on the faces consist of six protomers (hexons), while capsomeres that make up the vertices consist of five protomers (pentons). The precise numbers of protomers and the diameter of the virus particle are functions of the size of the genome. Icosahedral viruses include the papilloma (wart) viruses, poliovirus, rhinoviruses (common cold), and herpes viruses. The herpesviruses also contain an external envelope. The largest viruses, including the poxviruses, exhibit a more complex structure that is neither helical nor icosahedral. The poxviruses also contain complex internal structures.

The viral capsid in many viruses is enclosed within a lipid membrane called the envelope. With the exception of the poxviruses, the envelope is derived entirely from host cell membranes. Viruses such as the herpesviruses, which replicate in the nucleus of the cell, acquire an envelope by budding through the inner nuclear membrane. Viruses such as influenza and measles obtain their envelope by budding through cytoplasmic membranes. Viral envelopes usually have protein projections, viral encoded spikes or peplomers, on their surface that determine the host range for the virus. For example, influenza viruses have two sets of spikes embedded within their envelopes: the hemagglutinin (H) antigen protein, which attaches the virus to the target cell, and a neuraminidase (N) protein, which is used for release from the cell.

Viral Genomes

The structures of viral genetic molecules encompass numerous categories. Viral genomes may be either single-stranded DNA (parvoviruses, which are associated with fifth disease in humans), double-stranded DNA (adenoviruses and herpesviruses), single-stranded RNA (poliovirus, influenza, measles, rabies, and human immunodeficiency virus), or double-stranded RNA (rotaviruses). The genome in some RNA viruses may consist of a single segment (poliovirus, measles, and rabies) or may consist of multiple individual segments (influenza and rotaviruses). The genome in human immunodeficiency virus (HIV) is diploid, consisting of two identical copies of the RNA. The Baltimore classification scheme used to categorize or classify viruses is based on the type of genome and its replication strategy.

Viral Infection

Viral infection begins with the adsorption of the particle to the host cell, with the variety of targets referred to as the host range. Attachment is dependent upon the interaction between viral surface molecules and specific receptors on the target cell. Cells that lack such receptors cannot be infected by that virus. For example, HIV infects a class of lymphocytes called T cells that express the CD4 receptor protein. The rhinoviruses attach to a molecule on the surface of respiratory mucosal tissues called the intercellular adhesion molecule-1 (ICAM-1). Influenza H antigen attaches to a class of carbohydrates on the surface of respiratory cells. Most viruses are species-specific, infecting members only within the same species. Influenza virus is an exception. Because many organisms, including humans and birds, express the same carbohydrates on respiratory tissues, influenza has a wide host range that crosses species lines.

The ability of a virus to infect specific tissues is dependent on the expression of receptors by the host cell, leading to the question of why evolution does not select for cells that no longer express those receptor molecules. The answer lies in why cells express such receptors in the first place. The molecule is required for normal functions of the cell, particularly in its interactions with other cells. For example, the CD4 HIV receptor on T lymphocytes is critical for lymphocyte interactions with other classes of white blood cells. ICAM-1 molecules likewise facilitate cell-cell interactions and serve as a signal mediator in immune functions.

Attachment is followed by penetration of the viral capsid into the cell. If the virus has an envelope, the fusion of the viral and cell membranes, analogous to two oil droplets fusing, allows the capsid to penetrate the cell cytoplasm. Alternatively, if the virus lacks an envelope (and sometimes with viruses that do contain an envelope), the particle enters through a process called endocytosis, in which the cell membrane flows around or “envelops” the attached viral particle. Once inside the cell, the capsid is disassembled, releasing the genome. DNA viruses, such as the herpes viruses, generally travel to the nucleus for replication, while RNA viruses, such as poliovirus and rhinoviruses, replicate in the cytoplasm.

Viral Multiplication

Once the viral capsid has been disassembled, the expression and replication of the viral genome begin. The process used by DNA viruses differs from that in the replication of RNA viruses; cells already contain the basic machinery for the replication and expression of DNA, while no cellular enzymes are present for the replication of RNA.

The proteins necessary for duplication (DNA polymerases, DNA ligases, and other auxiliary molecules) and transcription (RNA polymerase) of viral DNA are already present in the nucleus of the cell. The processes of viral DNA replication and expression differ little from those that normally take place in the cell, and for smaller viruses cellular proteins are sufficient. Some larger viruses, such as the herpesviruses and poxviruses, have the genetic capacity to encode some of their own replication enzymes. For example, both herpesviruses and poxviruses synthesize their own specific DNA polymerases and are not dependent on the cellular enzymes.

Transcription and translation of genetic material immediately following infection results in the production of proteins utilized in the duplication of viral DNA. These are referred to as early genes, reflecting the timing of their expression. Genes expressed after DNA duplication are referred to as late genes and primarily encode structural or capsid proteins.

Because the cell lacks any machinery for duplication of RNA, RNA viruses must encode their own enzymes for duplication of their genetic material. The Baltimore classification scheme for RNA viruses roughly classifies these viruses on the nature or polarity of the RNA genome. Messenger RNA (mRNA), the RNA that is directly translated by cell ribosomes into protein, is defined as having a positive (+) polarity; RNA that is complementary to mRNA is defined as a minus (-) polarity. The + and - symbols here refer only to the orientation of the molecule and do not reflect a positive or negative charge. Positive-stranded viruses have a genome that is identical to mRNA, while minus- or negative-stranded viruses possess a genome that is complementary to their mRNA.

Positive-stranded RNA viruses include the rhinoviruses, poliovirus, hepatitis A virus, and some of the mosquito-borne encephalitis viruses. Following entry into the cell and removal of the capsid, the RNA immediately attaches cell ribosomes and begins the process of translation of viral proteins. Among the enzymes being synthesized is a viral-specific RNA transcriptase used to replicate the viral genome.

The category of negative-stranded RNA viruses includes the influenza viruses; measles, mumps, and rubella viruses; and rabies virus. Because the RNA is complementary to mRNA, it cannot be directly translated following cell penetration. Negative-stranded viruses incorporate the viral transcriptase directly into the progeny capsids during assembly. Following infection, the viral mRNA is then transcribed by the RNA transcriptase, which the virus carries. The transcriptase also functions in copying the positive mRNA into the progeny (or negative) strands for the next generation of viral particles.

HIV, the etiological agent of acquired immunodeficiency syndrome (AIDS), is in an unusual class of viruses called the retroviruses. Other viruses in this class include the RNA tumor viruses, the agents associated with tumors and leukemia primarily in nonhuman animals. The genome in the retrovirus is a diploid plus-stranded RNA. However, the genome does not function directly as the mRNA following infection. The particle carries within its capsid an enzyme referred to as a reverse transcriptase, the function of which is to copy the RNA genome into a double-stranded DNA. The viral DNA integrates within the host cell chromosome from which the viral mRNA is transcribed, producing capsid proteins and copies of the reverse transcriptase enzyme for progeny virions.

Assembly and Release

Viral assembly is largely nonenzymatic and results from charge interactions among the structural proteins that make up the capsomeres. Animal viruses begin the assembly process in the region of the cell in which replication of the genome has taken place: RNA viruses in the cytoplasm and DNA viruses in the nucleus of the cell. Expression of the genes for structural proteins occurs primarily after the genome has been replicated. Capsid assembly begins as individual capsomeres commence forming scaffolds around the progeny genomes. The complexity of the process depends upon the coding capacity of the virus; larger and more complex viruses utilize a greater variety of assembly proteins, while smaller viruses may utilize only two or three protein molecules. The assembly of protein capsids is generally associated with a final cleavage step, in which capsid precursor proteins are cut to produce the final protein products.

Assembly and release of enveloped particles require an additional step: budding through a cell membrane. Some viruses, such as measles and influenza, encode a matrix or membrane protein (M) and those proteins that make up the spikes. The matrix and spikes are then inserted into the cell membrane. Assembly of the capsid is completed in association with the M protein, followed by a reverse endocytosis (exocytosis) as the virus buds through the membrane and acquires the envelope. Budding and release of influenza virus requires activity of the viral neuraminidase (N protein) that separates the envelope proteins on progeny viruses that would otherwise remain attached to carbohydrate residues on the cell surface. Some anti-influenza drugs act by inhibiting this enzyme activity. Maturation of the HIV capsid also requires a final proteolytic step using a viral encoded protease. Certain anti-HIV drugs target this reaction.

The effect of viral infection on the cell itself depends upon two factors: the extent of damage to the cell and whether cell processes are shut down. Productive infection by DNA viruses usually results in cell death. Viral products inhibit both transcription and translation of cell proteins, and release of progeny virions coincides with cell lysis. Alternatively, herpesvirus infections may result in a latent infection in which the virus does not carry out a complete cycle and is retained in a nonreplicative form within the cell. The cell remains functional while the virus is carried by the human host throughout their life. Enveloped viruses are released from the cell by budding through the cell membrane, a process that may damage or kill the host cell. The complete replication cycle for RNA viruses generally takes place in twelve to twenty-four hours, whereas DNA viruses require a slightly longer time, ranging from twenty-four to forty-eight hours.

Impact

Viruses are a class of strict intracellular parasites. Unlike bacteria, viruses are largely devoid of metabolic and enzymatic reactions and are, therefore, dependent on enzymes and other molecules provided by the host cell. For decades following the discovery of viruses, experts believed the inert nature and dependence of viruses on host functions precluded the development of antibiotics specifically targeting these organisms. However, in 1967, Joseph Kates and Brian McAuslan reported the presence of a viral polymerase in the capsid of poxviruses. In subsequent years, numerous viral encoded enzymes were discovered in infected cells, including the reverse transcriptase, an enzyme that copies viral genomic RNA into complementary DNA in cells infected with HIV and with RNA tumor viruses. The presence of enzymes and other molecules unique to viruses and required for their replication meant that antiviral compounds targeting viruses specifically could be developed.

Because many viruses utilize their own encoded polymerases for replication of their genomes, the first generation of antiviral antibiotics targeted these molecules. DNA analogs such as acyclovir and ganciclovir, molecules resembling normal nucleotides but that block genome replication, proved effective in treating herpesvirus infections. Amantadine was shown to block influenza virus infection and has proven effective in treating that illness. Two of the drugs targeting influenza, zanamivir and Tamiflu, act at the level of virus release, inhibiting the cleavage reaction involving the viral neuraminidase.

Several generations of drugs have been effective in controlling HIV replication. These include DNA analogs such as zidovudine (or azidothymidine, AZT), cytosine, arabinoside, pentostatin, fludarabine, and nelarabine, as well as protease inhibitors, such as fosamprenavir and leupeptin, that block the assembly of the virus. Although viruses do utilize host macromolecules for replication, the production of molecules unique to the virus has provided an opportunity for the application of antiviral drugs.

As scientists further understand the structure, life cycle, and replication functions of viruses, medications and therapeutic strategies are developed to better treat human ailments and prevent treatment-resistant strains of viruses from forming. For example, while developing vaccinations for COVID-19, scientists gained insight into RNA packaging and replication processes that informed the creation of innovative treatment and prevention therapies.

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